| Class | Genus | Species No. | Strain No. |
|---|---|---|---|
| Choanoflagellatea | Salpingoeca | 1 | 1 |
| Sarcomonadea | Sandona | 9 | 12 |
| Chlorophyceae | Scenedesmus | 7 | 12 |
| Schizocladiophyceae | Schizocladia | 1 | 1 |
| Dinophyceae | Scrippsiella | 1 | 3 |
| Cyanophyceae | Scytonema | 2 | 3 |
| Cyanophyceae | Scytonematopsis | 1 | 1 |
| Chlorophyceae | Selenastrum | 1 | 1 |
| Bacillariophyceae | Sellaphora | 1 | 3 |
| Bacillariophyceae | Skeletonema | 9 | 19 |
| Cyanophyceae | Sphaerospermopsis | 5 | 36 |
| Zygnematophyceae | Sphaerozosma | 1 | 1 |
| Zygnematophyceae | Spinoclosterium | 1 | 1 |
| Zygnematophyceae | Spirogyra | 13 | 15 |
| Cyanophyceae | Spirulina | 1 | 4 |
| Chrysophyceae | Spumella | 1 | 1 |
| Cyanophyceae | Stanieria | 1 | 1 |
| Zygnematophyceae | Staurastrum | 5 | 5 |
| Chlorophyceae | Stauridium | 1 | 1 |
| Zygnematophyceae | Staurodesmus | 1 | 1 |
| Bacillariophyceae | Staurosirella | 1 | 1 |
| Chlorophyceae | Stephanosphaera | 1 | 2 |
| Trebouxiophyceae | Stichococcus | 2 | 4 |
| Chlorophyceae | Stigeoclonium | 3 | 3 |
| Cyanophyceae | Stigonema | 1 | 1 |
| Placididea | Suigetsumonas | 1 | 1 |
| Heterokontophyta incertae sedis | Sulcochrysis | 1 | 1 |
| Dinophyceae | Symbiodinium | 1 | 8 |
| Bicoecea | Symbiomonas | 1 | 1 |
| Cyanophyceae | Symploca | 1 | 1 |
| Cyanophyceae | Synechococcus | 2 | 61 |
| Cyanophyceae | Synechocystis | 1 | 2 |
| Chrysophyceae | Synura | 3 | 5 |
| Coccolithophyceae | Syracosphaera | 1 | 2 |
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